Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing

Results show the minimum sequencing depth required for the discovery of differentially methylated regions at desired sensitivity and specificity and the trade-off between adding more replicates versus increasing sequencing depth. Whole-genome bisulfite sequencing (WGBS) allows genome-wide DNA methylation profiling, but the associated high sequencing costs continue to limit its widespread application. We used several high-coverage reference data sets to experimentally determine minimal sequencing requirements. We present data-derived recommendations for minimum sequencing depth for WGBS libraries, highlight what is gained with increasing coverage and discuss the trade-off between sequencing depth and number of assayed replicates.